Bert's Blog australis

Bert's Blog australis

| | |

Main interests are molecular biology, cancer biology and space sciences

Genome sequencing applied to cancer

9/28/2006

Thomas et al. have published a paper in Nature Medicine (available for free from the Roche Applied Science site) in which the Genome Sequencer 20 is used to sequence DNA from tumours to find novel genetic changes. This is a powerful tool for cancer medicine.

Prior to this, discovery of novel genetic changes in a cancer would have required a lot of work looking at specific genes. This "shotgun" approach is not only sensitive but also semi-quantitative.

I highly recommend reading of this paper.

0 Comments | Post Comment | Permanent Link

Multilineage involvement of the fusion gene in patients with FIP1L1/PDGFRA-positive HES

1/17/2006

British Journal of Haematology
Volume 132 Page 286 - February 2006
doi:10.1111/j.1365-2141.2005.05863.x

Volume 132 Issue 3

Multilineage involvement of the fusion gene in patients with FIP1L1/PDGFRA-positive hypereosinophilic syndrome

Jamie Robyn¹, Steven Lemery², J. Philip McCoy³, Joseph Kubofcik⁴, Yae-Jean Kim⁴, Svetlana Pack⁵, Thomas B. Nutman⁴, Cynthia Dunbar² and Amy D. Klion⁴

Summary

Myeloproliferative hypereosinophilic syndrome (MHES) is a disorder characterised by male predominance, marked eosinophilia, splenomegaly, tissue fibrosis, elevated serum tryptase and the presence of the FIP1L1/PDGFRA fusion gene in peripheral blood mononuclear cells. The characteristic hypercellular bone marrow with dysplastic eosinophils and spindle-shaped mast cells suggest that multiple lineages may be involved in the clonal process. To determine which haematopoietic lineages are involved in MHES, we purified cells of specific lineages from patients with MHES and used nested reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR and fluorescence in situ hybridisation to analyse the purified cell populations for the presence of the fusion gene. The fusion gene was detected in eosinophils, neutrophils, mast cells, T cells, B cells and monocytes. These results suggest that the mutation arises in a pluripotential haematopoietic progenitor cell capable of giving rise to multiple lineages. The basis for the preferential expansion of eosinophils and mast cells remains unclear.

0 Comments | Post Comment | Permanent Link

super sequencer : behind the technology that sequenced the mammoth genome

1/12/2006

The Nature paper describes the "454 Life Sciences' Genome Sequencer 20 System" pictured below:

Genomicists Webb Miller and Stephan C. Schuster in front of the Roche / 454 Life Sciences' Genome Sequencer 20 System that was used to sequence mammoth nuclear DNA.

http://www.sciencemag.org/cgi/content/abstract/1123360v1

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Hendrik N. Poinar ¹^*, Carsten Schwarz ², Ji Qi ³, Beth Shapiro ⁴, Ross D. E. MacPhee ⁵, Bernard Buigues ⁶, Alexei Tikhonov ⁷, Daniel Huson ⁸, Lynn P. Tomsho ³, Alexander Auch ³, Markus Rampp ⁹, Webb Miller ³, Stephan C. Schuster ³^*

¹ McMaster Ancient DNA Center; Department of Anthropology; Pathology & Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
² McMaster Ancient DNA Center; Department of Anthropology
³ Penn State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA.
⁴ Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK.
⁵ Division of Vertebrate Zoology/Mammalogy American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024, USA.
⁶ #2 Avenue de la Pelouse, F-94160 St Mandé France.
⁷ Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.1, Saint-Petersburg 199034, Russia.
⁸ Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany.
⁹ Garching Computing Center (RZG), Boltzmannstrasse 2, D-85748 Garching, Germany.

^* To whom correspondence should be addressed.
Hendrik N. Poinar , E-mail: poinarh@mcmaster.ca
Stephan C. Schuster , E-mail: scs@bx.psu.edu

We sequenced 28 million base pairs of DNA in a metagenomicsapproach using a woolly mammoth (Mammuthus primigenius) samplefrom Siberia. Thanks to exceptional sample preservation and use of a novel emulsion polymerase chain reaction and pyrosequencingtechnique, 13 million base pairs (45.4%) of the sequencing readswere identified as mammoth DNA. Sequence identity between ourdata and African elephant (Loxodonta africana) was 98.55%, consistentwith a paleontologically based divergence date of 5 to 6 millionyears. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverablefrom this single mammoth would allow for completion of its genome,unleashing the field of paleogenomics.